uk.ac.ebi.intact.application.intSeq.business
Class ManagerFilesBlast

java.lang.Object
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  +--uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
        |
        +--uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast

public class ManagerFilesBlast

extends ManagerFiles

This class inherits the ManagerFiles class. The particular output file of the Blast program needs a non-generic method for its parsing. Usually, the wu-blast method requires this method, but sometimes, the ncbi-blast gives the same output file, when the option "-m 9" is not used in the command line. This option makes a table output format, which needs a generic method defined in the ManagerFiles class, which parses a table.

Version:

: $Id: ManagerFilesBlast.java,v 1.3 2003/07/16 13:56:24 skerrien Exp $

Author:

shuet (shuet@ebi.ac.uk)

Field Summary

Fields inherited from class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles

absolutePath, fileName

Constructor Summary

ManagerFilesBlast()
constructor by default

ManagerFilesBlast(java.lang.String pathFile, java.lang.Object extension)
constructor which allows us to create a random file name, this application is multi-user.

ManagerFilesBlast(java.lang.String pathFile, java.lang.String fileName)
constructor which passes a hard file name in parameter

Method Summary

java.util.ArrayList

ResultParsing(java.util.ArrayList patterns, int jWhichGroup) This method parses a wu-blast output file, to retrieve the accession number of each result, the percentage identity with the query, start and end of the both aligned fragments.

Methods inherited from class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles

CreateFile, CreateWriter, DeleteFile, GetFileName, GetLineSeparator, GetPathFile, GetRandFileName, ParseWithReAllFollow, ParseWithReOneGroup, PrepareBufferedReader, PutInFile, ReadingFile, ResultParsingTableFile, SetFileName, SetPathFile

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ManagerFilesBlast

public ManagerFilesBlast()

constructor by default

ManagerFilesBlast

public ManagerFilesBlast(java.lang.String pathFile,
                         java.lang.Object extension)

constructor which allows us to create a random file name, this application is multi-user. So, it allows to reduce possible conflicts.

Parameters:

pathFile - String to know where to put this file

extension - Object representing the logic extension behind the file name

ManagerFilesBlast

public ManagerFilesBlast(java.lang.String pathFile,
                         java.lang.String fileName)

constructor which passes a hard file name in parameter

Parameters:

pathFile - String to know where to put this file

fileName - String to represent the hard name file

Method Detail

ResultParsing

public java.util.ArrayList ResultParsing(java.util.ArrayList patterns,
                                         int jWhichGroup)
                                  throws IntactException

This method parses a wu-blast output file, to retrieve the accession number of each result, the percentage identity with the query, start and end of the both aligned fragments. --------------- WU-BLAST OUTPUT FILE SAMPLE -------------------------------- >SWALL:O88613 (3873) MUSCARINIC ACETYLCHOLINE RECEPTOR M1 (FRAGMENT) Length = 200 Score = 61 (26.5 bits), Expect = 4.4, Sum P(2) = 0.99 Identities = 26/78 (33%), Positives = 36/78 (46%) Query: 317 TEKQARELSVPQG---PGAGAESTGEIINNTVPLENSI---PGNCCSALFKNLLLK---- 366 TE +AREL+ QG PG G S+ + E S PG CC LL+ Sbjct: 58 TENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPESPPGRCCRCCRTPRLLQAYSW 117 Query: 367 KIKRCERKGT-ESVTEEK 383 K + E +G+ ES+T + Sbjct: 118 KEEEEEDEGSMESLTSSE 135 Score = 37 (18.1 bits), Expect = 4.4, Sum P(2) = 0.99 Identities = 7/14 (50%), Positives = 8/14 (57%) Query: 655 PLPTPELQMPTMVP 668 P+ PE Q PT P Sbjct: 148 PMVDPEAQAPTKQP 161 >SWALL:O55068 (3829) ALPHA1B-ADRENERGIC RECEPTOR (FRAGMENT) Length = 85 Score = 51 (23.0 bits), Expect = 5.6, P = 0.996 Identities = 13/33 (39%), Positives = 19/33 (57%) Query: 164 SLIETPANGTGPSEALAMLLQETTGELEAAKAL 196 +L T A G P ++A+ L + + E EAAK L Sbjct: 47 TLSSTKAKGHNPRSSIAVKLFKFSREKEAAKTL 79 What is retrieved from this file by the regular expression is described in the file where the regular expression is defined (the SeqIdConstant class temporarily -- later in a configuration file of the application)

Overrides:

ResultParsing in class ManagerFiles

Parameters:

patterns - contains the Regular Expression list, one for each item to retrieve.

jWhichGroup - defines the group requiered in the regular expression: jWhichGroup must be different from "0" otherwise, the whole line is retrieved.

Returns:

The result is a list (all lines retrieved) of lists (all items retrieved in one line).

IntactException